The city was founded in the 11th century as Murustage but has origins going back to Punic and Roman times. In 1516 it was captured by the Ottoman admiral Barbarossa and became a centre for Mediterranean sea corsairs, as well as a commercial port. By 1700 it had come under Ottoman rule and in 1833 the city was taken by France and a garrison established. Algeria became independent in 1962.

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Mostaganem corresponds to the ancient Punic port of Murustaga. After becoming part of the Roman Empire, it was, according to some sources, officially renamed Cartennae under the emperor Gallienus (253–268).[2] However, according to more weighty sources, Cartennae (or Cartenna or Cartennas) corresponds instead to modern Ténès, 50 km to the east.[3][4] In any case, Murustaga is the name by which the town was known when it became a Christian bishopric, and by which it is referred to in the Catholic Church's list of episcopal sees.[5] It also underlies the modern name of Mostaganem.

The city is divided in two by a ravine of the river Aïn Sefra, with the modern town to southwest, and the old Muslim city, Tidgit, to the northeast.

In 2010 a tunnel moving under the city towards the city centre is expected to change circulation by a lot. Also, new buildings, some modern and some in colonial style are being added to this growing city. The new autoroute from the capital Algiers towards Oran will make it easier also to access Mostaganem by road from the capital, as Mostaganem has no public airport. The road connecting Oran (around 80 km from Mostaganem to the west) will remain the same, a crowded 2 lane in each direction highway.

The port of Mostaganem is being used for unloading of all sorts of cargo, ranging from provisions to cars and pipelines. As in most ports of Algeria, it is not allowed to sailors to exit the port and visit the city. The port is being shared by large transport vessels and fishing boats alike. A new, smaller port for fishing boats has been constructed, but is currently not used.

Furthermore, one of the most notable religious figures of the 20th century was also born and later buried in Mostaganem, the Great Sufi Master, Ahmad al-Alawi, who played a major role in spreading the ShadhiliDarqawi tariqa (spiritual order) across the globe, such that this order is now considered one of the world's largest and most influential Sufi paths. Many modern Muslims consider al-Alawi to be one of the "revivers" of Islam in the 20th century due to his role in spreading the religion, and even influencing the West, including opening the first mosque in Paris. Al-Alawi's tomb is now a popular visitation sight in Mostaganem.